From aee79ab5f7477d9e1c75be61d8b51881debf90ed Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Mon, 16 Sep 2024 17:26:27 +0200 Subject: [PATCH] Update CHANGELOG.md --- CHANGELOG.md | 188 +++------------------------------------------------ 1 file changed, 8 insertions(+), 180 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2732a8a3..10416ede8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,185 +1,13 @@ -# Change Log +# Changelog -## 2.0.0 +This project's full changelog is maintained in the GitHub releases page. -### Main changes +For a comprehensive list of changes, new features, and bug fixes, please visit: https://github.com/DeepRank/deeprank2/releases. -#### Refactor +This page includes: -- refactor: make `preprocess` use all available feature modules as default by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/247 -- refactor: move preprocess function to `QueryDataset` class and rename by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/252 -- refactor: save preprocessed data into one .hdf5 file as default by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/250 -- refactor: clean up `GraphDataset` and `Trainer` class by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/255 -- refactor: reorganize deeprank2.utils.metrics module by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/262 -- refactor: fix `transform_sigmoid` logic and move it to `GraphDataset` class by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/288 -- refactor: add grid dataset class and make the trainer class work with it. by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/294 -- refactor: update deprecated dataloader import by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/310 -- refactor: move tests/\_utils.py to tests/**init**.py by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/322 -- refactor: delete all outputs from unit tests after run by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/324 -- refactor: test_contact.py function naming and output by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/372 -- refactor: split test contact.py by @joyceljy in https://github.com/DeepRank/deeprank-core/pull/369 -- refactor: change **repr** of AminoAcid to 3 letter code by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/384 -- refactor: make feature modules and tests uniform and ditch duplicate code by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/400 +- Detailed release notes for each version +- Summary of changes +- Links to relevant issues and pull requests -#### Features - -- feat: improve amino acid features by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/272 -- feat: add `test_size` equivalent of `val_size` to Trainer class by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/291 -- feat: add the option to have a grid box of different x,y and z dimensions by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/292 -- feat: add early stopping to `Trainer.train` by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/303 -- feat: add hist module for plotting raw hdf5 files features distributions by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/261 -- feat: allow for different loss functions other than the default by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/313 -- feat: center the grids as in the old deeprank by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/323 -- feat: add data augmentation for grids by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/336 -- feat: insert features standardization option in`DeeprankDataset` children classes by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/326 -- feat: add log transformation option for plotting features' hist by @joyceljy in https://github.com/DeepRank/deeprank-core/pull/389 -- feat: add inter-residue contact (IRC) node features by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/333 -- feat: add feature module for secondary structure by @DTRademaker in https://github.com/DeepRank/deeprank-core/pull/387 -- feat: use dictionary for flexibly transforming and standardizing features by @joyceljy in https://github.com/DeepRank/deeprank-core/pull/418 - -#### Fix - -- fix: list all submodules imported from deeprank2.features using pkgutil by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/263 -- fix: let `classes` argument be also categorical by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/286 -- fix: makes sure that the `map_feature` function can handle single value features. by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/289 -- fix: raise exception for invalid optimizer by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/307 -- fix: `num_workers` parameter of Dataloader object by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/319 -- fix: gpu usage by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/334 -- fix: gpu and `entry_names` usage by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/335 -- fix: data generation threading locked by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/330 -- fix: `__hash__` circular dependency issue by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/341 -- fix: make sure that Grid data also has target values, like graph data by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/347 -- fix: change the internal structure of the grid data to match the graph data by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/352 -- fix: conflicts in package by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/386 -- fix: correct usage of nonbond energy for close contacts by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/368 -- fix: Incorrect number of datapoints loaded to model by @joyceljy in https://github.com/DeepRank/deeprank-core/pull/397 -- fix: pytorch 2.0 by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/406 -- fix: covalent bonds cannot link nodes on separate branches by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/408 -- fix: `Trainer` error when only `dataset_test` and `pretrained_model` are used by @ntxxt in https://github.com/DeepRank/deeprank-core/pull/413 -- fix: check PSSMs by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/401 -- fix: only check pssms if conservation module was used by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/425 -- fix: epoch number in `test()` and test on the correct model by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/427 -- fix: convert list of arrays into arrays before converting to Pytorch tensor by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/438 - -#### Docs - -- docs: add verbose arg to QueryCollection class by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/267 -- docs: improve `clustering_method` description and default value by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/293 -- docs: uniform docstrings format in modules by @joyceljy -- docs: incorrect usage of Union in Optional type hints by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/370 -- docs: improve docs for default exporter and results visualization by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/414 -- docs: update feature documentations by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/419 -- docs: add instructions for `GridDataset` by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/421 -- docs: fix getstarted hierarchy by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/422 -- docs: update dssp 4 install instructions by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/437 -- docs: change `external_distance_cutoff` and `interface_distance_cutoff` to `distance_cutoff` by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/246 - -#### Performances - -- perf: features.contact by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/220 -- perf: suppress warnings in pytest and from PDBParser by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/249 -- perf: add try except clause to `_preprocess_one_query` method of `QueryCollection` class by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/264 -- perf: improve `process` speed for residue based graph building by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/274 -- perf: add `cuda` and `ngpu` parameters to the `Trainer` class by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/311 -- perf: accelerate indexing of HDF5 files by @joyceljy in https://github.com/DeepRank/deeprank-core/pull/362 - -#### Style - -- style: restructure deeprank2 package and subpackages by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/240 -- style: reorganize features/contact.py by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/260 -- style: add .vscode settings.json by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/404 - -#### Test - -- test: make sure that the grid orientation is as in the original deeprank for `ProteinProteinInterfaceAtomicQuery` by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/312 -- test: check that the grid for residue-based protein-protein interfaces has the same center and orientation as in the original deeprank. by @cbaakman in https://github.com/DeepRank/deeprank-core/pull/339 -- test: improve `utils/test_graph.py` module by @gcroci2 in https://github.com/DeepRank/deeprank-core/pull/420 - -#### CI - -- ci: do not close stale issues or PRs by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/327 -- ci: remove incorrect message for stale branches by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/415 -- ci: automatically check markdown links by @DaniBodor in https://github.com/DeepRank/deeprank-core/pull/433 - -### New Contributors - -- @joyceljy made their first contribution in https://github.com/DeepRank/deeprank-core/pull/361 -- @ntxxt made their first contribution in https://github.com/DeepRank/deeprank-core/pull/413 - -**Full Changelog**: https://github.com/DeepRank/deeprank-core/compare/v1.0.0...v2.0.0 - -## 1.0.0 - -Released on Oct 24, 2022 - -### Added - -- `weight_decay` parameter to NeuralNet #155 -- Exporter for generating a unique .csv file containing results per epoch #151 -- Automatized testing of all available features modules #163 -- `optimizer` parameter to NeuralNet #154 -- `atom` node feature #168 - -### Changed - -- `index` parameter of NeuralNet is now called `subset` #159 -- `percent` parameter of NeuralNet is now called `val_size`, and the logic behing it has been improved #183 -- Aligned the package to PyTorch high-level frameworks #172 - - NeuralNet is now called Trainer -- Clearer features names #145 -- Changed definitions in storage.py #150 -- `MAX_COVALENT_DISTANCE` is now 2.1 instead of 3 #205 - -### Removed - -- `threshold` input parameter from NeuralNet #157 - -## 0.2.0 - -Released on Aug 10, 2022 - -### Added - -- Automatic version bumping using `bump2version` with `.bumpversion.cfg` #126 -- `cffconvert.yml` to the CI workflow #139 -- Integration test for the Machine Learning pipeline #95 -- The package now is tested also on Python 3.10 #165 - -### Changed - -- Test PyPI package before publishing, by triggering a `workflow_dispatch` event from the Actions tab on `release.yml` workflow file #123 -- Coveralls is now working again #124 -- Wrong Zenodo entry has been corrected #138 -- Improved CUDA support (added for data tensors) #132 - -## 0.1.1 - -Released on June 28, 2022 - -### Added - -- Graph class #48 -- Tensorboard #15 -- CI Linting #30 -- Name, affiliation and orcid to `.zenodo.json` #18 -- Metrics class #17 -- QueryDataset class #53 -- Unit tests for NeuralNet class #86 -- Error message if you pick the wrong metrics #110 -- Unit tests for HDF5Dataset class parameters #82 -- Installation from PyPI in the readme #122 - -### Changed - -- `test_process()` does not fail anymore #47 -- Tests have been speded up #36 -- `multiprocessing.Queue` has been replaced with `multiprocessing.pool.map` in PreProcessor #56 -- `test_preprocess.py` does not fail anymore on Mac M1 #74 -- It's now possible to pass your own train/test split to NeuralNet class #81 -- HDF5Dataset class now is used in the UX #83 -- IndexError running `NeuralNet.train()` has been fixed #89 -- pip installation has been fixed -- Repository has been renamed deeprank-core, and the package deeprank2 #101 -- The zero-division like error from TensorboardBinaryClassificationExporter has been fixed #112 -- h5xplorer is installed through `setup.cfg` file #121 -- Sphinx docs have been fixed #108 +For any questions or to report issues, please use the [GitHub issues page](https://github.com/DeepRank/deeprank2/issues).